static void free_config() { free_if_not_null((void**)&am_conf_app_title); free_if_not_null((void**)&am_conf_app_id); free_if_not_null((void**)&am_conf_app_version); free_if_not_null((void**)&am_conf_app_shortname); free_if_not_null((void**)&am_conf_app_org); }
int parser_clear_data_buffers(parser_t *self) { free_if_not_null(self->stream); free_if_not_null(self->words); free_if_not_null(self->word_starts); free_if_not_null(self->line_start); free_if_not_null(self->line_fields); return 0; }
static void free_config() { free_if_not_null((void**)&am_conf_app_title); free_if_not_null((void**)&am_conf_app_author); free_if_not_null((void**)&am_conf_app_id); free_if_not_null((void**)&am_conf_app_version); free_if_not_null((void**)&am_conf_app_shortname); free_if_not_null((void**)&am_conf_app_display_name); free_if_not_null((void**)&am_conf_app_dev_region); free_if_not_null((void**)&am_conf_app_supported_languages); free_if_not_null((void**)&am_conf_app_icon); free_if_not_null((void**)&am_conf_app_launch_image); }
/* ---------------- sub_mat_destroy --------------------------- */ void sub_mat_destroy (struct sub_mat *s) { free_if_not_null (s->comment); free (s->fname); free (s); }
/* ---------------- kill_f_matrix ----------------------------- */ void kill_f_matrix ( float **matrix) { if ( ! matrix) return; free_if_not_null (matrix[0]); free (matrix); }
/* ---------------- kill_uc_matrix ---------------------------- */ void kill_uc_matrix ( unsigned char **matrix) { if ( ! matrix) return; free_if_not_null (matrix[0]); free (matrix); }
int parser_cleanup(parser_t *self) { if (self->cb_cleanup(self->source) < 0) { return -1; } if (parser_clear_data_buffers(self) < 0) { return -1; } // XXX where to put this free_if_not_null(self->error_msg); free_if_not_null(self->warn_msg); if (self->skipset != NULL) kh_destroy_int64((kh_int64_t*) self->skipset); return 0; }
/* ---------------- kill_i_matrix ----------------------------- */ void kill_i_matrix ( int **matrix, size_t n_rows) { size_t i; if ( ! matrix) return; for(i=0; i<n_rows; i++) free_if_not_null (matrix[i]); free (matrix); }
/* ---------------- prob_vec_destroy -------------------------- */ void prob_vec_destroy ( struct prob_vec *p_vec) { const char *this_sub = "prob_vec_destroy"; extern const char *prog_bug; extern const char *null_point; if ( ! p_vec ) { err_printf (this_sub, prog_bug, __FILE__, __LINE__); err_printf (this_sub, null_point); return; } free_if_not_null (p_vec->cmpct_n); free_if_not_null (p_vec->cmpct_prob); free_if_not_null (p_vec->cmpct_ndx); if (p_vec->mship) kill_f_matrix (p_vec->mship); free (p_vec); }
/* ---------------- dme_thresh -------------------------------- * We are given two sets of coordinates, probably coming from * the same molecule. Unfortunately, one may be imcomplete. This * is the model. We assume that all of its residues are present * in the larger structure. * Begin by building a mask which can be applied to the larger * system. We will calculate a distance matrix only for the * residues present in both molecules. * Our return value is success/failure, but our numerical return * is via a pointer to a float. */ int dme_thresh (float *frac, struct coord *c1, struct coord *c2, float thresh) { struct coord *ref, *mdl; char *ref_mask; struct dme_res result; struct dmat ref_dmat, mdl_dmat; if (c1->size > c2->size) ref = c1, mdl = c2; else ref = c2, mdl = c1; if (mdl->size <= 1) { /* If given a tiny model, should we return */ *frac = 0.0; /* failure or success ? */ return EXIT_SUCCESS; /* There is no correct answer. Depends on what */ } /* caller expects */ ref_mask = dmat_make_mask(mdl, ref); alloc_dmat (&ref_dmat, mdl->size); /*same as model size - not a bug ! */ alloc_dmat (&mdl_dmat, mdl->size); fill_dmat (&ref_dmat, ref, mdl->size, ref_mask); fill_dmat (&mdl_dmat, mdl, mdl->size, NULL); result = get_dme (ref_dmat, mdl_dmat, thresh); del_dmat (&ref_dmat); del_dmat (&mdl_dmat); free_if_not_null (ref_mask); *frac = (float) result.n_left / result.sz; return EXIT_SUCCESS; }
int recursively_install(char* pkg_name, char* pkg_version, char* install_root_name, char* link_to_root, char* overlay_path, int is_upgrade, int overwrite_config, int overwrite_other_package_files, char* tmp_dir, opkg_conf* conf, string_map* package_data, string_map* install_called_pkgs) { int err=0; /* variables not allocated in this function, do not need to be freed */ string_map* install_pkg_data = get_package_with_version(package_data, pkg_name, pkg_version); char* src_file_path = get_string_map_element(install_pkg_data, "Install-File-Location"); char* src_id = get_string_map_element(install_pkg_data, "Source-ID"); char* pkg_filename = get_string_map_element(install_pkg_data, "Filename"); string_map* pkg_dependencies = get_string_map_element(install_pkg_data, "Required-Depends"); char* install_root_path = get_string_map_element(conf->dest_names, install_root_name); char* link_root_path = link_to_root != NULL && safe_strcmp(link_to_root, install_root_name) != 0 ? get_string_map_element(conf->dest_names, link_to_root) : NULL; char* base_url = NULL; /* variables that may need to be freed */ char* pkg_dest = NULL; string_map* files_to_link = NULL; char* info_dir = NULL; char* control_name_prefix = NULL; char* list_file_name = NULL; string_map* conf_files = NULL; string_map* copied_conf_files = NULL; int install_root_len = strlen(install_root_path); char* fs_terminated_install_root = install_root_path[install_root_len-1] == '/' ? strdup(install_root_path) : dynamic_strcat(2, install_root_path, "/"); int overlay_root_len; char* fs_terminated_overlay_root = NULL; if(overlay_path != NULL) { overlay_root_len = strlen(overlay_path); fs_terminated_overlay_root = overlay_path[overlay_root_len-1] == '/' ? strdup(overlay_path) : dynamic_strcat(2, overlay_path, "/"); } else { fs_terminated_overlay_root = strdup(fs_terminated_install_root); } int link_root_len; char* fs_terminated_link_root = NULL; if(link_root_path != NULL) { link_root_len = strlen(link_root_path); fs_terminated_link_root = link_root_path[link_root_len-1] == '/' ? strdup(link_root_path) : dynamic_strcat(2, link_root_path, "/"); } set_string_map_element(install_called_pkgs, pkg_name, strdup("D")); if(pkg_dependencies != NULL) { //recurse unsigned long num_deps; char** deps = get_string_map_keys(pkg_dependencies, &num_deps); int dep_index; for(dep_index=0; err == 0 && dep_index < num_deps ; dep_index++) { if(get_string_map_element(install_called_pkgs, deps[dep_index]) == NULL ) { char** dep_def = get_string_map_element(pkg_dependencies, deps[dep_index]); int is_current; char* matching_version; string_map* dep_pkg = get_package_current_or_latest_matching(package_data, deps[dep_index], dep_def, &is_current, &matching_version); if(dep_pkg != NULL) { char* dep_status = get_string_map_element(dep_pkg, "Status"); if(strstr(dep_status, " half-installed") != NULL) { err = recursively_install(deps[dep_index], matching_version, install_root_name, link_to_root, overlay_path, is_upgrade, overwrite_config, overwrite_other_package_files, tmp_dir, conf, package_data, install_called_pkgs); } } else { err = 1; } } } } if(install_root_path == NULL || ( src_id == NULL && install_pkg_data == NULL) || (pkg_filename == NULL && install_pkg_data == NULL) ) { //sanity check err = 1; } if(err == 0) { printf("Preparing to install package %s...\n", pkg_name); } if(err == 0 && src_file_path == NULL) { //determine source url string_map* src_lists[2] = { conf->gzip_sources, conf->plain_sources }; int src_list_index; for(src_list_index=0; src_list_index < 2 && base_url == NULL; src_list_index++) { base_url = (char*)get_string_map_element(src_lists[src_list_index], src_id); } err = base_url == NULL ? 1 : err; if(err == 1) { fprintf(stderr, "ERROR: Could determine download URL for package %s\n", pkg_name); } } if(err == 0 && src_file_path == NULL) { //download package printf("\tDownloading...\n"); char* src_url = dynamic_strcat(3, base_url, "/", pkg_filename); pkg_dest = dynamic_strcat(3, tmp_dir, "/", pkg_name); FILE* package_file = fopen(pkg_dest, "w"); if(package_file != NULL) { err = write_url_to_stream(src_url, "gpkg", NULL, package_file, NULL); fclose(package_file); } else { err = 1; } if(err == 1) { fprintf(stderr, "ERROR: Could not download package %s\n", pkg_name); } free(src_url); } if(err == 0 && src_file_path != NULL) { pkg_dest = strdup(src_file_path); } if(err == 0 && src_file_path == NULL) { //check md5sum char* md5sum = file_md5sum_alloc(pkg_dest); char* expected_md5sum = (char*)get_string_map_element(install_pkg_data, "MD5Sum"); //printf("md5sum = %s\n", md5sum); //printf("package md5sum = %s\n", (char*)get_string_map_element(install_pkg_data, "MD5Sum")); if(md5sum == NULL || expected_md5sum == NULL) { fprintf(stderr, "ERROR: Expected MD5Sum for %s not specified, cannot verify package\n", pkg_name); err = 1; } else if (safe_strcmp(md5sum, expected_md5sum) != 0) { fprintf(stderr, "ERROR: MD5Sum mismatch for %s package\n", pkg_name); fprintf(stderr, " Expected: %s\n", expected_md5sum); fprintf(stderr, " Downloaded: %s\n\n", md5sum); err = 1; } else { printf("\tDownloaded %s successfully.\n\tInstalling %s...\n", pkg_name, pkg_name); } if(md5sum != NULL) { free(md5sum); } } if(err == 0) { // Extract list file contaiing list of files to install info_dir = dynamic_strcat(2, fs_terminated_overlay_root, "usr/lib/opkg/info"); control_name_prefix = dynamic_strcat(4, info_dir, "/", pkg_name, "."); list_file_name = dynamic_strcat(4, info_dir, "/", pkg_name, ".list"); mkdir_p(info_dir, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH ); FILE* list_file = fopen(list_file_name, "w"); deb_extract( pkg_dest, list_file, extract_quiet | extract_data_tar_gz | extract_list, NULL, NULL, &err); fclose(list_file); if(err) { rm_r(list_file_name); fprintf(stderr, "ERROR: could not extract file list from packge %s.\n", pkg_name); fprintf(stderr, " package file may be corrupt\n\n"); } } if(err == 0) { //extract control files deb_extract( pkg_dest, stderr, extract_control_tar_gz | extract_all_to_fs| extract_preserve_date | extract_unconditional, control_name_prefix, NULL, &err); if(err) { fprintf(stderr, "ERROR: could not extract control files from packge %s.\n", pkg_name); fprintf(stderr, " package file may be corrupt\n\n"); } } if(err == 0) { //check for file conflicts & correct list file to contain real root name in file paths unsigned long num_list_lines; char** list_file_lines = get_file_lines(list_file_name, &num_list_lines); char* conf_file_path = dynamic_strcat(4, info_dir, "/", pkg_name, ".conffiles"); if(path_exists(conf_file_path)) { unsigned long num_conf_lines; char** conf_file_lines = get_file_lines(conf_file_path, &num_conf_lines); int conf_line_index; conf_files = initialize_string_map(1); for(conf_line_index=0; conf_line_index < num_conf_lines; conf_line_index++) { char* adjusted_conf_path = dynamic_strcat(2, fs_terminated_install_root, conf_file_lines[conf_line_index] + 1); set_string_map_element(conf_files, adjusted_conf_path, strdup("D")); free(adjusted_conf_path); } free_null_terminated_string_array(conf_file_lines); } free(conf_file_path); FILE* list_file = fopen(list_file_name, "w"); int line_index; for(line_index=0; line_index < num_list_lines && (!err) ; line_index++) { int line_len = strlen( list_file_lines[line_index] ); if(line_len > 2) { if(list_file_lines[line_index][0] == '.' && list_file_lines[line_index][1] == '/' && list_file_lines[line_index][line_len-1] != '/') { char* adjusted_file_path = dynamic_strcat(2, fs_terminated_install_root, list_file_lines[line_index] + 2); int is_conf_file = conf_files != NULL ? (get_string_map_element(conf_files, adjusted_file_path) != NULL ? 1 : 0) : 0; if(strcmp(pkg_name, "opkg") == 0 && strcmp(list_file_lines[line_index], "./bin/opkg") == 0 && path_exists("/bin/opkg") == PATH_IS_SYMLINK) { //very special case: we're installing opkg, and here all the preliminary checks have already been passed //remove symlink placeholder to gpkg from /bin/opkg if it exists rm_r("/bin/opkg"); } err = path_exists(adjusted_file_path) && is_conf_file == 0 && overwrite_other_package_files == 0 ? 1 : 0; if(err) { fprintf(stderr, "ERROR: file '%s'\n", adjusted_file_path); fprintf(stderr, " from package %s already exists.\n\n", pkg_name); } else { fprintf(list_file, "%s\n", adjusted_file_path); if(link_root_path != NULL) { char* link_to_path = dynamic_strcat(2, fs_terminated_link_root, list_file_lines[line_index] + 2); files_to_link = files_to_link == NULL ? initialize_string_map(1) : files_to_link; set_string_map_element(files_to_link, adjusted_file_path, link_to_path); //don't free link_to_path, should be freed with files_to_link map } if(is_conf_file && path_exists(adjusted_file_path) && overwrite_config == 0) { char* tmp_conf_path = dynamic_strcat(2, tmp_dir, adjusted_file_path); cp(adjusted_file_path, tmp_conf_path); copied_conf_files = copied_conf_files == NULL ? initialize_string_map(1) : copied_conf_files; set_string_map_element(copied_conf_files, adjusted_file_path, tmp_conf_path); //don't free tmp_conf_path, should be freed with copied_conf_files map } } free(adjusted_file_path); } } } fclose(list_file); if(list_file_lines != NULL) { free_null_terminated_string_array(list_file_lines); } } if(err == 0) { //run preinst err = run_script_if_exists(install_root_path, link_root_path, pkg_name, "preinst", (is_upgrade ? "upgrade" : "install") ); } if(err == 0) { //extract package files deb_extract( pkg_dest, stderr, extract_data_tar_gz | extract_all_to_fs| extract_preserve_date| extract_unconditional, fs_terminated_overlay_root, NULL, &err); if(err) { fprintf(stderr, "ERROR: could not extract application files from packge %s.\n", pkg_name); fprintf(stderr, " package file may be corrupt\n\n"); } //move any conf files back if(copied_conf_files != NULL) { unsigned long num_conf_paths; char** conf_paths = get_string_map_keys(copied_conf_files, &num_conf_paths); int conf_index; for(conf_index=0; conf_index < num_conf_paths; conf_index++) { char* tmp_conf_path = get_string_map_element(copied_conf_files, conf_paths[conf_index]); cp(tmp_conf_path, conf_paths[conf_index]); } destroy_string_map(copied_conf_files, DESTROY_MODE_FREE_VALUES, &num_conf_paths); if(conf_paths != NULL ) { free_null_terminated_string_array(conf_paths); } copied_conf_files = NULL; } } if(err == 0 && files_to_link != NULL) { unsigned long num_files; char** real_files = get_string_map_keys(files_to_link, &num_files); int file_index; if(num_files > 0) { char* link_file_name = dynamic_strcat(4, info_dir, "/", pkg_name, ".linked"); FILE* link_file = fopen(link_file_name, "w"); for(file_index=0; link_file != NULL && file_index < num_files; file_index++) { char* link_path = get_string_map_element(files_to_link, real_files[file_index]); if(!path_exists(link_path)) { int sym_success; mkdir_p(link_path, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH ); rm_r(link_path); sym_success = symlink(real_files[file_index], link_path); fprintf(link_file, "%s\n", link_path); } } if(link_file != NULL) { fclose(link_file); } free(link_file_name); } destroy_string_map(files_to_link, DESTROY_MODE_FREE_VALUES, &num_files); free_null_terminated_string_array(real_files); files_to_link = NULL; } if(err == 0) { //run postinst int warn = run_script_if_exists(install_root_path, link_root_path, pkg_name, "postinst", (is_upgrade ? "upgrade" : "install") ); if(warn != 0) { fprintf(stderr, "Warning: postinstall script failed for package %s.\n", pkg_name); } } if(err == 0) { // remove downloaded package file in tmp dir & print success if(src_file_path == NULL) { rm_r(pkg_dest); } printf("\tSuccessfully installed %s.\n", pkg_name); } //cleanup unsigned long num_destroyed; free_if_not_null(pkg_dest); free_if_not_null(info_dir); free_if_not_null(control_name_prefix); free_if_not_null(list_file_name); free_if_not_null(fs_terminated_install_root); free_if_not_null(fs_terminated_overlay_root); free_if_not_null(fs_terminated_link_root); if(files_to_link != NULL) { destroy_string_map(files_to_link, DESTROY_MODE_FREE_VALUES, &num_destroyed); } if(conf_files != NULL) { destroy_string_map(conf_files, DESTROY_MODE_FREE_VALUES, &num_destroyed); } if(copied_conf_files!= NULL){ destroy_string_map(copied_conf_files, DESTROY_MODE_FREE_VALUES, &num_destroyed); } return err; }
//void do_install(opkg_conf* conf, char* pkg_name, char* install_root_name, char* link_root_name, char** version_criteria) void do_install(opkg_conf* conf, string_map* pkgs, char* install_root_name, char* link_root_name, int is_upgrade, int overwrite_config, int overwrite_other_package_files, int force_reinstall, char* tmp_root) { string_map* package_data = initialize_string_map(1); string_map* matching_packages = initialize_string_map(1); string_map* pkgs_from_file = initialize_string_map(1); unsigned long num_destroyed; char* install_root_path = (char*)get_string_map_element(conf->dest_names, install_root_name); char* overlay_path = NULL; // no special treatment of overlay, can be reenabled by setting this variable here if we ever need it char* test_dir = dynamic_strcat(2, (overlay_path != NULL ? overlay_path : install_root_path), "/usr/lib/opkg/info"); if(!create_dir_and_test_writable(test_dir)) { fprintf(stderr, "ERROR: Specified install destination is not writable, exiting\n"); exit(1); } free(test_dir); if(install_root_path == NULL) { printf("ERROR: No destination %s found, cannot install\n\n", install_root_name); exit(1); } char* tmp_dir = (char*)malloc(1024); if(create_tmp_dir(tmp_root == NULL ? "/tmp" : tmp_root, &tmp_dir) != 0) { fprintf(stderr, "ERROR: Could not create tmp dir, exiting\n"); exit(1); } /* Determine all packages to install by first loading all package names, status & dependencies (and no other variables) */ load_all_package_data(conf, package_data, matching_packages, NULL, LOAD_MINIMAL_PKG_VARIABLES_FOR_ALL, install_root_name, 1, NULL ); destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed); /* determine list of all packiages we are about to install, including dependencies */ string_map* install_pkgs_map = initialize_string_map(1); char** install_pkg_list = NULL; unsigned long install_pkg_list_len = 0; char* unsatisfied_dep_err = NULL; /* new string map var with all pkgs to install = pkgs, keys = version */ unsigned long num_pkg_names; char** pkg_names = get_string_map_keys(pkgs, &num_pkg_names); int pkg_name_index; /* * Load data for any packages being installed via ipk and * determine if any packages we are about to install * provide anything, and if so set package we are installing to preferred */ string_map* preferred_provides = initialize_string_map(1); for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++) { char* pkg_name = pkg_names[pkg_name_index]; char** version_criteria = get_string_map_element(pkgs, pkg_name); char* install_pkg_version = NULL; int install_pkg_is_current; /* deal with case where we're installing from file */ if(path_exists(pkg_name)) { //installing from file char* pkg_file = pkg_name; //extract control files int err = 0; char* tmp_control = dynamic_strcat(2, tmp_dir, "/tmp_ctrl"); char* tmp_control_prefix = dynamic_strcat(2, tmp_control, "/tmp."); char* tmp_control_name = dynamic_strcat(2, tmp_control_prefix, "control"); mkdir_p(tmp_control, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH ); deb_extract( pkg_file, stderr, extract_control_tar_gz | extract_all_to_fs| extract_preserve_date | extract_unconditional, tmp_control_prefix, NULL, &err); if(err != 0) { fprintf(stderr, "ERROR: %s is not a valid package file, cannot install\n", pkg_file); rm_r(tmp_dir); exit(1); } string_map* tmp_control_pkg_data = initialize_string_map(1); matching_packages = initialize_string_map(1); load_package_data(tmp_control_name, 0, tmp_control_pkg_data, matching_packages, NULL, LOAD_ALL_PKG_VARIABLES, NULL, NULL); unsigned long num_ctrl_names; char** ctrl_name_list = get_string_map_keys(tmp_control_pkg_data, &num_ctrl_names); destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed); err = 1; //set back to 0 when data successfully loaded if(num_ctrl_names > 0) { int ctrl_name_index; for(ctrl_name_index=0; ctrl_name_list[ctrl_name_index] != NULL; ctrl_name_index++) { if( strcmp(ctrl_name_list[ctrl_name_index], PROVIDES_STRING) != 0) { pkg_name = strdup(ctrl_name_list[ctrl_name_index]); } } char* version = NULL; int is_current; string_map* pkg_info = get_package_current_or_latest(tmp_control_pkg_data, pkg_name, &is_current, &version); if(pkg_info != NULL) { err = 0; set_string_map_element(pkg_info, "Install-File-Location", strdup(pkg_file)); set_string_map_element(pkg_info, "Version", version); //we need to save this, since we are going to set a special version to make sure data doesn't get over-written later, also no need to free version now char* special_version = dynamic_strcat(2, version, "@@_FILE_INSTALL_VERSION_@@"); char** new_version_criteria = malloc(3*sizeof(char*)); new_version_criteria[0] = strdup("="); new_version_criteria[1] = special_version; new_version_criteria[2] = NULL; version_criteria = new_version_criteria; string_map* all_current_versions = get_string_map_element(package_data, pkg_name); if(all_current_versions == NULL) { all_current_versions=initialize_string_map(1); set_string_map_element(package_data, pkg_name, all_current_versions); } set_string_map_element(all_current_versions, special_version, pkg_info); set_string_map_element(all_current_versions, LATEST_VERSION_STRING, special_version); free(pkg_names[pkg_name_index]); pkg_names[pkg_name_index] = strdup(pkg_name); set_string_map_element(pkgs, pkg_name, copy_null_terminated_string_array(new_version_criteria)); set_string_map_element(pkgs_from_file, pkg_name, strdup("D")); } } free_null_terminated_string_array(ctrl_name_list); if(err != 0) { fprintf(stderr, "ERROR: %s is not a valid package file, cannot install\n", pkg_file); rm_r(tmp_dir); exit(1); } free_if_not_null(tmp_control); free_if_not_null(tmp_control_prefix); free_if_not_null(tmp_control_name); rm_r(tmp_control); } /* determine if package provides anything, and set this package to preferred if so*/ string_map* install_pkg_data = get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version); if(install_pkg_data != NULL) { char* provides_str = get_string_map_element(install_pkg_data, "Provides"); if(provides_str != NULL) { if(strlen(provides_str) > 0) { unsigned long num_provides; char package_separators[] = {' ', ',', ':', ';', '\'', '\"', '\t', '\r', '\n'}; char** provides_list = split_on_separators(provides_str, package_separators, 9, -1, 0, &num_provides); int provides_index; char* provides_unique_key = dynamic_strcat(3, pkg_name, "@", install_pkg_version); for(provides_index=0; provides_index < num_provides; provides_index++) { char* provides_name = strdup(provides_list[provides_index]); char* eq = strchr(provides_name, '='); if(eq != NULL) { *eq = '\0' ; } if(strlen(provides_name) > 0) { set_string_map_element(preferred_provides, provides_name, strdup(provides_unique_key)); } } } } } } /* reload with new preferred_provides */ free_recursive_package_vars(package_data); matching_packages = initialize_string_map(1); load_all_package_data(conf, package_data, matching_packages, NULL, LOAD_MINIMAL_PKG_VARIABLES_FOR_ALL, install_root_name, 1, preferred_provides ); destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed); /* load data and do sanity checks for packages we are about to install */ for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++) { char* pkg_name = pkg_names[pkg_name_index]; char** version_criteria = get_string_map_element(pkgs, pkg_name); char* install_pkg_version = NULL; int install_pkg_is_current; load_recursive_package_data_variables(package_data, pkg_name, 1, 0, 0); // load required-depends for package of interest only string_map* install_pkg_data = get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version); char* install_status = install_pkg_data == NULL ? NULL : get_string_map_element(install_pkg_data, "Status"); if(install_status != NULL) { char** old_el = set_string_map_element(install_pkgs_map, pkg_name, copy_null_terminated_string_array(version_criteria) ); if(old_el != NULL){ free_null_terminated_string_array(old_el); } string_map* install_pkg_depend_map = get_string_map_element(install_pkg_data, "Required-Depends"); if(install_pkg_depend_map != NULL) { unsigned long num_keys; char** load_detail_pkgs = get_string_map_keys(install_pkg_depend_map, &num_keys); int ldp_index; for(ldp_index=0;ldp_index < num_keys && unsatisfied_dep_err == NULL; ldp_index++) { char* dep_name = load_detail_pkgs[ldp_index]; char** dep_def= get_string_map_element(install_pkg_depend_map, dep_name); if(get_string_map_element(install_pkgs_map, dep_name) != NULL) { /* * We really should check here whether old dependency def can be reconciled with the new one, and report an error if it can't * Right now we just use the heuristic that top-level (user specified, not dependency) package defs get preference, followed * by first dependency encountered. * * Since right now versioning features aren't really being used very much other than kernel dependencies in Gargoyle/OpenWrt * I'm just leaving this comment here as a reminder that this should be addressed at some point rather than messing with it now * */ dep_def = get_string_map_element(install_pkgs_map, dep_name); } else { set_string_map_element(install_pkgs_map, dep_name, copy_null_terminated_string_array(dep_def)); } //error checking, check that dependency definition exists char* latest_version = NULL; int latest_is_current = 0; string_map* dep_info = get_package_current_or_latest_matching(package_data, dep_name, dep_def, &latest_is_current, &latest_version); //check if we have a version installed different than what is required int have_current; char* current_version = NULL; string_map* cur_info = get_package_current_or_latest(package_data, dep_name, &have_current, ¤t_version); if(have_current && (latest_is_current == 0 || dep_info == NULL)) { //should only get here if dep_def[1] is not null (version mismatch doesn't make sense if no version is specified) char* cur_status = get_string_map_element(cur_info, "Status"); if(strstr(cur_status, " hold ") != NULL) { unsatisfied_dep_err = dynamic_strcat(11, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " is installed,\n\t\tbut has incompatible version ", current_version, " and is marked as 'hold'"); } else { unsatisfied_dep_err = dynamic_strcat(10, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " is installed,\n\t\tbut has incompatible version ", current_version); } } free_if_not_null(current_version); free_if_not_null(latest_version); // check that dependency definition exists if(unsatisfied_dep_err == NULL && dep_info == NULL) { if(dep_def[1] != NULL) { unsatisfied_dep_err = dynamic_strcat(9, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " cannot be found, try updating your package lists"); } else { unsatisfied_dep_err = dynamic_strcat(5, "ERROR: Dependency ", dep_name, " of package ", pkg_name, " cannot be found, try updating your package lists"); } } } free_null_terminated_string_array(load_detail_pkgs); } } install_status = install_pkg_data == NULL ? NULL : get_string_map_element(install_pkg_data, "Status"); /* error checking before we start install */ if(install_pkg_data == NULL || install_status == NULL) { fprintf(stderr, "ERROR: No package named %s found, try updating your package lists\n\n", pkg_name); rm_r(tmp_dir); exit(1); } if(strstr(install_status, " installed") != NULL) { if(force_reinstall) { fprintf(stderr, "WARNING: Package %s is already installed, forcing removal and reinstallation\n\n", pkg_name); free_package_data(package_data); string_map* rm_pkg = initialize_string_map(1); set_string_map_element(rm_pkg, pkg_name, alloc_depend_def(NULL)); do_remove(conf, rm_pkg, (overwrite_config ? 0 : 1), 0, 1, 0, tmp_root); //restart install return do_install(conf, pkgs, install_root_name, link_root_name, is_upgrade, overwrite_config, overwrite_other_package_files, force_reinstall, tmp_root); } else { fprintf(stderr, "WARNING: Package %s is already installed, ignoring\n", pkg_name); fprintf(stderr, " Use --force-reinstall to force reinstallation\n\n"); char** old_el = remove_string_map_element(install_pkgs_map, pkg_name); if(old_el != NULL){ free_null_terminated_string_array(old_el); }; } } if(unsatisfied_dep_err != NULL) { fprintf(stderr, "%s\n", unsatisfied_dep_err); rm_r(tmp_dir); exit(1); } } /* load more detailed data on packages we are about to install */ free_recursive_package_vars(package_data); /* note: whacks install_pkg_depend_map */ string_map* parameters = initialize_string_map(1); matching_packages = initialize_string_map(1); set_string_map_element(parameters, "package-list", install_pkgs_map); load_all_package_data(conf, package_data, matching_packages, parameters, LOAD_MINIMAL_FOR_ALL_PKGS_ALL_FOR_MATCHING, install_root_name, 0, preferred_provides); unsigned long from_file_pkg_list_len; char** from_file_pkg_list = get_string_map_keys(pkgs_from_file, &from_file_pkg_list_len); int from_file_index; for(from_file_index=0; from_file_index < from_file_pkg_list_len; from_file_index++) { char* old = set_string_map_element(matching_packages, from_file_pkg_list[from_file_index], strdup("D")); free_if_not_null(old); } free_null_terminated_string_array(from_file_pkg_list); install_pkg_list = get_string_map_keys(matching_packages, &install_pkg_list_len); destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed); destroy_string_map(parameters, DESTROY_MODE_IGNORE_VALUES, &num_destroyed); char* all_pkg_list_str = join_strs(", ", install_pkg_list, install_pkg_list_len, 0, 0); uint64_t combined_size = 0; int pkg_index; for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++) { char** match_criteria = get_string_map_element(install_pkgs_map, install_pkg_list[pkg_index]); string_map* pkg = get_package_current_or_latest_matching(package_data, install_pkg_list[pkg_index], match_criteria, NULL, NULL); char* next_size_str = get_string_map_element(pkg, "Installed-Size"); uint64_t next_size = 0; if(sscanf(next_size_str, SCANFU64, &next_size) > 0) { combined_size = combined_size + next_size; } } uint64_t root_size = destination_bytes_free(conf, install_root_name); if(combined_size >= root_size ) { fprintf(stderr, "ERROR: Not enough space in destination %s to install specified packages:\n\t%s\n\n", install_root_name, all_pkg_list_str); rm_r(tmp_dir); exit(1); } if(all_pkg_list_str != NULL) { printf("Preparing to install the following packages, which will require " SCANFU64 " bytes:\n\t%s\n\n", combined_size, all_pkg_list_str); } else { fprintf(stderr, "No packages to install.\n\n"); } /* Set status of new required packages to half-installed, set user-installed on requested package, installed time on all */ char* install_root_status_path = dynamic_strcat(2, install_root_path, "/usr/lib/opkg/status"); string_map* install_root_status = initialize_string_map(1); matching_packages = initialize_string_map(1); if(path_exists(install_root_status_path)) { load_package_data(install_root_status_path, 0, install_root_status, matching_packages, NULL, LOAD_ALL_PKG_VARIABLES, install_root_name, preferred_provides); } destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed); time_t now = time(NULL); char install_time[20]; sprintf(install_time, "%lu", now); for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++) { int is_installed; char* install_version = NULL; char** match_criteria = get_string_map_element(install_pkgs_map, install_pkg_list[pkg_index]); string_map* pkg = get_package_current_or_latest_matching(package_data, install_pkg_list[pkg_index], match_criteria, &is_installed, &install_version); if(is_installed == 0) /* should never be true, but check anyway */ { char* old_status = remove_string_map_element(pkg, "Status"); free(old_status); char* status_parts[3] = { "install", "ok", "half-installed" }; status_parts[1] = get_string_map_element(pkgs, install_pkg_list[pkg_index]) != NULL ? "user" : status_parts[1]; char* new_status = dynamic_strcat(5, status_parts[0], " ", status_parts[1], " ", status_parts[2]); set_string_map_element(pkg, "Status", new_status); set_string_map_element(pkg, "Installed-Time", strdup(install_time)); set_string_map_element(pkg, "Install-Destination", strdup(install_root_name)); if(link_root_name != NULL) { set_string_map_element(pkg, "Link-Destination", strdup(link_root_name)); } add_package_data(install_root_status, &pkg, install_pkg_list[pkg_index], install_version, NULL); /* Note: we just added pkg data structure from package_data to install_root_status, Be careful on cleanup! */ } } save_package_data_as_status_file(install_root_status, install_root_status_path); string_map* install_called_pkgs = initialize_string_map(1); int err = 0; for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++) { char* pkg_name = pkg_names[pkg_name_index]; if(get_string_map_element(install_pkgs_map, pkg_name) != NULL && get_string_map_element(install_called_pkgs, pkg_name) == NULL) { int install_pkg_is_current; char* install_pkg_version = NULL; char** version_criteria = get_string_map_element(pkgs, pkg_name); get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version); err = recursively_install(pkg_name, install_pkg_version, install_root_name, link_root_name, overlay_path, is_upgrade, overwrite_config, overwrite_other_package_files, tmp_dir, conf, package_data, install_called_pkgs); free_if_not_null(install_pkg_version); } } if(err) { fprintf(stderr, "An error occurred during Installation, removing partially installed packages.\n"); unsigned long num_install_called_pkgs; char** install_called_pkg_list = get_string_map_keys(install_called_pkgs, &num_install_called_pkgs); int pkg_index; for(pkg_index=0; pkg_index < num_install_called_pkgs; pkg_index++) { remove_individual_package(install_called_pkg_list[pkg_index], conf, package_data, tmp_dir, 0, 0); } free_null_terminated_string_array(install_called_pkg_list); //call remove function to do cleanup of partial install //DO NOT EXIT HERE, fixup status file below } //remove tmp dir -- need to do this whether or not there is an error rm_r(tmp_dir); free(tmp_dir); //set status of new packages to installed on success, and remove on failure for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++) { /* no need to check version, should only be one installed version at a time... */ string_map* pkg = get_package_current_or_latest(install_root_status, install_pkg_list[pkg_index], NULL, NULL); if(pkg != NULL) { if(!err) { char* status = get_string_map_element(pkg, "Status"); if(strstr(status, " half-installed") != NULL) { char* status_parts[3] = { "install", "ok", "installed" }; status_parts[1] = get_string_map_element(pkgs, install_pkg_list[pkg_index]) != NULL ? "user" : status_parts[1]; char* new_status = dynamic_strcat(5, status_parts[0], " ", status_parts[1], " ", status_parts[2]); char* old_status = set_string_map_element(pkg, "Status", new_status); free_if_not_null(old_status); } } else { string_map* all_pkg_versions = remove_string_map_element(install_root_status, install_pkg_list[pkg_index]); free_all_package_versions(all_pkg_versions); } } } save_package_data_as_status_file(install_root_status, install_root_status_path); if(!err) { if(all_pkg_list_str != NULL) { printf("Installation of packages successful.\n\n"); } } else { printf("Finished removing partially installed packages.\n\n"); } }
/* ---------------- seq_strct_2_duplicated_prob_vec ----------------------- * Duplikate the pvec while structure estimation and also duplicate the sequence, * each n-times. * return: * struct prob_vec *pvec * Notice: not used, but who knows if it will became useful one day ! * (Martin May, 2007) */ struct prob_vec * strct_2_duplicated_prob_vec (struct coord *structure, const struct seq *seq, const struct seqprof *sp, const size_t size, const struct aa_strct_clssfcn *cmodel, const size_t n_duplications) { size_t i, j; float *fragment; struct prob_vec *pvec; float **aa_prob; struct aa_clssfcn *aa_class; const size_t n_pvec = size - cmodel->n_att + 1; if ((pvec = new_pvec (cmodel->n_att, n_duplications * size , n_duplications * n_pvec, cmodel->strct->n_class))!= NULL) { for (i = 0; i < (n_duplications * n_pvec); i++) /* Initialize mship */ for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] = cmodel->strct->class_weight[j]; if (structure) { /* Structure membership */ for (i = 0; i < n_pvec; i++){ /* for every fragment...*/ /* twice for every fragment on position i as on i + size */ fragment = getFragment (i , cmodel->n_att, structure); for (j = 0; j < n_duplications; j++){ if (computeMembershipStrct(pvec->mship[ i + j * n_pvec], fragment, cmodel->strct) == NULL) { prob_vec_destroy (pvec); return NULL; } } } free_if_not_null (fragment); } if (sp || seq) { /* Sequence or profile membership */ aa_prob = f_matrix (n_duplications * n_pvec, cmodel->strct->n_class); aa_class = E_MALLOC (sizeof (struct aa_clssfcn)); aa_class->n_class = cmodel->strct->n_class; aa_class->n_att = cmodel->n_att; aa_class->log_pp = cmodel->log_pp; aa_class->class_wt = cmodel->strct->class_weight; if (seq){ struct seq *s = seq_duplicate ( seq , n_duplications ); if (computeMembershipAA (aa_prob, s, aa_class) == EXIT_FAILURE) { prob_vec_destroy (pvec); return NULL; } seq_destroy (s); } else if (sp) { if (computeMembershipAAProf (aa_prob, sp, aa_class) == EXIT_FAILURE) { prob_vec_destroy (pvec); return NULL; } } free (aa_class); for (i = 0; i < n_duplications * n_pvec; i++) for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] *= aa_prob[i][j]; kill_f_matrix (aa_prob); } for (i = 0; i < (n_duplications * n_pvec); i++){ double sum = 0.0; for (j = 0; j < cmodel->strct->n_class; j++) sum += pvec->mship[i][j]; for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] /= sum; } pvec->norm_type = PVEC_TRUE_PROB; } return pvec; }
/* ---------------- seq_strct_2_prob_vec ----------------------- * This calculates probabilities for using combinations of * sequence and structure, sequence profile and structure, * sequence only, sequence profile only, and structure only. */ static struct prob_vec * seq_strct_2_prob_vec (struct coord *structure, const struct seq *seq, const struct seqprof *sp, const size_t size, const struct aa_strct_clssfcn *cmodel, const enum yes_no norm) { size_t i, j, compnd_len; float *fragment; struct prob_vec *pvec; float **aa_prob; struct aa_clssfcn *aa_class; const size_t n_pvec = size - cmodel->n_att + 1; if ((pvec = new_pvec (cmodel->n_att, size,n_pvec, cmodel->strct->n_class))!= NULL) { for (i = 0; i < n_pvec; i++) /* Initialize mship */ for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] = cmodel->strct->class_weight[j]; if (structure) { /* Structure membership */ for (i = 0; i < n_pvec; i++) { /* for every fragment...*/ fragment = getFragment (i, cmodel->n_att, structure); if (computeMembershipStrct(pvec->mship[i], fragment, cmodel->strct) == NULL) { prob_vec_destroy (pvec); return NULL; } } free_if_not_null (fragment); } if (sp || seq) { /* Sequence or profile membership */ aa_prob = f_matrix (n_pvec, cmodel->strct->n_class); aa_class = E_MALLOC (sizeof (struct aa_clssfcn)); aa_class->n_class = cmodel->strct->n_class; aa_class->n_att = cmodel->n_att; aa_class->log_pp = cmodel->log_pp; aa_class->class_wt = cmodel->strct->class_weight; if (seq){ struct seq *s = seq_copy (seq); if (computeMembershipAA (aa_prob, s, aa_class) == EXIT_FAILURE) { prob_vec_destroy (pvec); return NULL; } seq_destroy (s); } else if (sp) { if (computeMembershipAAProf (aa_prob, sp, aa_class) == EXIT_FAILURE) { prob_vec_destroy (pvec); return NULL; } } free (aa_class); for (i = 0; i < n_pvec; i++) for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] *= aa_prob[i][j]; kill_f_matrix (aa_prob); } if (norm == YES) { for (i = 0; i < n_pvec; i++){ double sum = 0.0; for (j = 0; j < cmodel->strct->n_class; j++) sum += pvec->mship[i][j]; for (j = 0; j < cmodel->strct->n_class; j++) pvec->mship[i][j] /= sum; } pvec->norm_type = PVEC_TRUE_PROB; } } /*shoffmann*/ compnd_len = structure->compnd_len; /*finally read compound*/ if(compnd_len > 0){ pvec->compnd = E_MALLOC(compnd_len*sizeof(char)); pvec->compnd = memmove(pvec->compnd, structure->compnd, compnd_len); } pvec->compnd_len = compnd_len; return pvec; }
/* ---------------- sub_mat_read ------------------------------ */ struct sub_mat * sub_mat_read (const char *fname) { # ifndef BUFSIZ # error please define BUFSIZ to around 1024 # endif fpos_t pos; struct sub_mat *smat = NULL; FILE *fp; char buf [BUFSIZ]; char aanames [ MAX_AA + 3]; const char *this_sub = "read_mat"; const char comment = '#'; if ((fp = mfopen (fname, "r", this_sub)) == NULL) return NULL; /* Portably initialise the fpos_t structure * because =0 is insufficient */ if (fgetpos(fp, &pos)) { mperror (this_sub); goto broken; } smat = E_MALLOC ( sizeof (*smat)); smat -> fname = NULL; smat -> comment = NULL; smat->fname = save_str (fname); while (fgets (buf, BUFSIZ, fp) != NULL) { if ( buf[0] != comment) { if (fsetpos (fp, &pos)) { mperror (this_sub); goto broken; } break; } smat->comment = save_str_append (smat->comment, buf); if (fgetpos(fp, &pos)) { mperror (this_sub); goto broken; } } if (fgets (buf, BUFSIZ, fp) == NULL) goto broken; memset (aanames, BAD_AA, MAX_AA); if (get_aa_names (aanames, buf, BAD_AA) == EXIT_FAILURE) goto broken; { int n, m; for (n = 0; n < MAX_AA; n++) for ( m = 0; m < MAX_AA; m++) smat->data[n][m] = (mat_t) INVALID; } { int n = 0; for ( ;fgets(buf, BUFSIZ, fp) != NULL; n++) { if (aanames [n] == BAD_AA) continue; if (add_to_mat (smat, aanames, buf, n) == EXIT_FAILURE) err_printf (this_sub, "Ignoring matrix line\n"); } } fclose (fp); return smat; broken: fclose (fp); free_if_not_null (smat->comment); free_if_not_null (smat->fname); free_if_not_null (smat); return NULL; }